2) Mother Brain
Featured In: Super Metroid (1994)
At the beginning of Super Metroid, Samus recaps her previous adventures and her battle with the Space Pirate leader, Mother Brain. Soon after you arrive on Zebes and head below the surface, you arrive at the very room you battled her in, and it fills you with a strange feeling of ominousness (if you played the first game or Zero Mission. Otherwise, it's just another room). Later, you discover the entrance to the new Tourian (Mother Brain's lair) after defeating the four Space Pirate commanders.
A few rooms later, you enter familiar territory: the exact same room you fought Mother Brain in has been recreated in the new Tourian. Confidently you blast your way past the Zebetite barriers and begin shattering the glass containing the oversized brain. Once you've pumped her full of enough missiles, the acid drains and her containment collapses. Satisfied with your accomplishment, you begin patting yourself on the back.
And then she gets back up, complete with a new body.
Despair begins to set in as you attempt to dodge her devastating attacks, only to realize that yours don't seem to be affecting her at all. Eventually, she decides to make you suffer and hits you with a beam that drains multiple energy tanks at a time. After a couple of these hits, Samus is unable to even stand up. Just as Mother Brain prepares the final attack, the Infant Metroid swoops in and latches on to her and drains her energy. It then proceeds to give you all of your energy back; unfortunately, Mother Brain revives herself and begins killing the Metroid. Rather than saving itself, the Metroid continues to heal you, and then attempts to attack Mother Brain again. This time, the attack is fatal, and the Metroid lets out a final shriek and dies.
For whatever reason, you are given the power that Mother Brain was using to drain your health in the form of the Hyper Beam, with completely decimates the cyborg. After you've dealt out enough punishment, her body is destroyed and the brain disintegrates into dust, and a final timer is activated which will destroy the entire planet. Zebes is destroyed, ending Mother Brain's threat forever. Kind of... Gotta play Other M to find out what I mean!
The reason this fight is so high is the sheer amount of different emotions you feel throughout it. From dread, to hope, to heartbreak, to the feeling of being a sheer badass, it's all here in this masterpiece of a boss battle.
2) Mother Brain (Super Metroid)
What's not to love about this fight. It's the final boss of the game! Mother brain, is well.....a giant brain. You fight her in her big glass jar just like the original Metroid, but after you beat her your not done. Oh no she then stands up with a huge robotic looking body and begins to waylay you. This fight overall really isn't that hard, but it's so much fun. Especially when you get the hyper beam, and can just go to town destroying her. That's why she's number 2.